#Loading libraries

Merged Seurat Object

#Loading merged seurat object

This analysis was carried out on the 3 experiments: 230303, 230320, 230327. In these experiments, we used OT-II Ptendel BALB/c mice, corresponding to OT-II Ptendel C57BL/6J(B6) mice crossed with BALB/c mice. Based on the clinical status of mice and FACS analysis we categorized the T cell leukemic development into three major stages: pre-leukemic ‘early’, pre-leukemic ‘late’ and leukemic. Then, we performed a CITE-seq assays on the thymus and spleen of 3 control OT-II BALB/c mice and 9 OT-II Ptendel BALB/c mice (1 mouse from ‘pre-leukemic’early ; 5 mice from pre-leukemic ’late’ and 3 mice from leukemic stages).

p1 <- VlnPlot(bc.combined.cc,features = "nFeature_RNA", group.by = "orig.ident", pt.size = 0.1) 
p2 <- VlnPlot(bc.combined.cc,features = "percent.ribo", group.by = "orig.ident", pt.size = 0.1) 
plot_grid(p1, p2, ncol = 2)

#Results of data demultiplexing

DimPlot(bc.combined.cc, group.by = "MULTI_ID", reduction = "wnn.umap", pt.size = 0.5, label = TRUE, repel = TRUE, label.size = 2.5)

#Leukemia stages

annotation.palette1 <- c("#ECD078FF","#DA5B43FF", "#C12942FF","#AF1900FF")
annotation.palette2 <- c("#80D0D0FF", "#50A8B0FF" , "#3870A0FF","#284878FF")
names(annotation.palette1) <- c("Thymus-WT","Thymus-PreTum early","Thymus-PreTum late","Thymus-Tum")
names(annotation.palette2) <- c("Spleen-WT","Spleen-PreTum early","Spleen-PreTum late","Spleen-Tum")
DimPlot(bc.combined.cc, group.by = "annotation", reduction = "wnn.umap",cols = c(annotation.palette1,annotation.palette2), pt.size = 0.2, label = TRUE, repel = T, label.size = 4, label.color = "#0D0C0BFF")

DimPlot(bc.combined.cc, group.by = "MULTI_ID", split.by = "annotation", reduction = "wnn.umap", pt.size = 0.2, label = TRUE, repel = T, label.size = 4,ncol=4, label.color = "#0D0C0BFF")

#Clustering

DimPlot(bc.combined.cc, group.by = "wsnn_res.2", reduction = "wnn.umap" , pt.size = 0.5, label = TRUE, repel = TRUE)

WT subset analysis
load(file = "/mnt/NASBIOINFO_CP/LALT/BIOINFO/PTEN/03_Analysis/Analysis2024/RObject/miceWT_2023_merged.Robj")
DefaultAssay(miceWT) <- 'RNA'
Idents(miceWT) <- "wsnn_res.0.6"
DimPlot(miceWT, reduction = "wnn.umap", group.by = "wsnn_res.0.6", label = T, label.size = 6)

FeaturePlot(miceWT, reduction = "wnn.umap", features = c("adt_CD25","Il2ra","Mki67","adt_CD8","adt_CD4","adt_CD3","adt_CD62L","adt_CD69","Myc","adt_TCRgd","Rag1","adt_CCR7")) & scale_colour_gradientn(colours = (viridis::rocket(10, direction = -1)))

Idents(miceWT)<-"wsnn_res.0.6"
miceWT@active.ident <- factor(miceWT@active.ident,levels=c("6","11","14","5","0","7","2","1","15","10","4","9","3","8","12","13"))
genes <- c("Ptcra","Il2ra","adt_CD25","Top2a","Mki67","Rag1","Cd3d","adt_CD3","Cd4","adt_CD4","Cd8a","adt_CD8","Ccr9","Cd69","adt_CD69","Ccr7","adt_CCR7","Sell","Nkg7","Gzma","Ccl5","Klrc1","Trdc","adt_TCRgd")
p3 <- DotPlot(miceWT, features = genes) + geom_point(aes(size=pct.exp), shape = 21, colour="black", stroke=0.5) + scale_colour_gradient2(low = "steelblue", mid = "ivory1", high = "red") + guides(size=guide_legend(override.aes=list(shape=21, colour="black", fill="white"))) + RotatedAxis() + coord_flip()+ labs(title = "Expression of marker genes by clusters")
p4 <- DimPlot(miceWT, reduction = "wnn.umap", group.by = "wsnn_res.0.6", label = T, label.size = 6) + labs(title = "UMAP Visualization of Clusters in WT Mice")
plot_grid(p3, p4, ncol = 2)

WT.palette <- c('#59A5A9FF', '#60AB9EFF', '#69B190FF', '#77B77DFF', '#8CBC68FF', '#A6BE54FF', '#BEBC48FF', '#D1B541FF', '#DDAA3CFF', '#E49C39FF', '#E78C35FF' )
names(WT.palette) <- c("DN", "DPsm-CD25+", "DPsm-CCR7+", "DPblast", "DPsm", "DP69int", "DP69+", "SP4","SP8", "Tgd", "NK")
DimPlot(miceWT,reduction = "wnn.umap", group.by = "manual.annotation", label = T, cols = WT.palette , pt.size = 0.2,label.size = 3 )

#ScigeneX reveals co-expressed gene modules across cell populations

# # Select informative genes
# miceWT_scigenex20.3 <- select_genes(miceWT,
#                               k = 20,
#                               distance_method = "pearson",
#                               which_slot = "data",
#                               row_sum=2)
# 
# # Run MCL
# miceWT_scigenex20.3 <- gene_clustering(miceWT_scigenex20.3,
#                                  s = 5,
#                                  threads = 2,
#                                  inflation = 3)
load(file= "/mnt/NASBIOINFO_CP/LALT/BIOINFO/PTEN/03_Analysis/Analysis2024/RObject/miceWT_scigenex20.3.Robj")
miceWT_scigenex20.3@gene_clusters
## $`1`
##   [1] "Ms4a4b"         "Gm2682"         "Klf2"           "H2-D1"         
##   [5] "H2-K1"          "AW112010"       "Gimap3"         "H2-Q6"         
##   [9] "B2m"            "Cnn2"           "Shisa5"         "Tmsb10"        
##  [13] "Gimap4"         "Ms4a6b"         "Itgb7"          "Fxyd5"         
##  [17] "Ccr7"           "Cd52"           "Cd53"           "S1pr1"         
##  [21] "Il7r"           "Ripor2"         "Hcst"           "Lcp1"          
##  [25] "B4galnt1"       "Sidt1"          "Gramd3"         "Samhd1"        
##  [29] "Tagln2"         "Evl"            "Slfn1"          "Vim"           
##  [33] "Klk8"           "Ccnd2"          "Rflnb"          "Cdk2ap2"       
##  [37] "Ltb"            "Inpp4b"         "Psme2"          "Bcl2"          
##  [41] "Cd2"            "Add3"           "Psmb9"          "Ifi27l2a"      
##  [45] "Cotl1"          "Kbtbd11"        "Gpr183"         "Anxa6"         
##  [49] "Atp1b3"         "Bin2"           "Gpr18"          "Stat1"         
##  [53] "Cxcr3"          "Sell"           "Ptpn18"         "Psme1"         
##  [57] "Srgn"           "Pik3cd"         "Tpst2"          "Irf1"          
##  [61] "Rasa3"          "Il27ra"         "Lfng"           "Smc6"          
##  [65] "Gm8369"         "Ifi47"          "Glipr2"         "Stat4"         
##  [69] "Cytip"          "Arl4c"          "Aldoa"          "Gm45552"       
##  [73] "Cd226"          "Pde2a"          "Ctss"           "Smpdl3a"       
##  [77] "Chd3"           "Sp100"          "Ppp1r18"        "Ppp3cc"        
##  [81] "Stk10"          "Bach2"          "Junb"           "Tapbp"         
##  [85] "Sema4a"         "Igfbp4"         "Dapl1"          "Il6ra"         
##  [89] "Ifi208"         "Vasp"           "Gimap5"         "Ly6a"          
##  [93] "Chd7"           "Cd82"           "Rapgef6"        "Clec2d"        
##  [97] "Prkch"          "Sgk1"           "Jak1"           "Ass1"          
## [101] "Atp8b4"         "BE692007"       "Msn"            "Esyt1"         
## [105] "Smad7"          "Emp3"           "Ostf1"          "Sntb1"         
## [109] "Arrb2"          "Pde3b"          "Phf11b"         "Selplg"        
## [113] "Arpc1b"         "Foxo1"          "Plaat3"         "Cmah"          
## [117] "Epsti1"         "Cd48"           "Dock10"         "Pced1b"        
## [121] "Itgb2"          "Tnfaip8l2"      "Itga4"          "Ttc39b"        
## [125] "Runx3"          "Tagap"          "Gstp3"          "Tes"           
## [129] "Arl6ip5"        "Jun"            "Cyth4"          "Sgms1"         
## [133] "Tnfsf8"         "Vsir"           "Ier2"           "Il10rb"        
## [137] "S1pr4"          "Fos"            "Ms4a6d"         "Myh9"          
## [141] "Tpm4"           "Pitpnc1"        "Scml4"          "Ndfip1"        
## [145] "Zfp36l2"        "Dtx1"           "Gimap7"         "Nlrc5"         
## [149] "Cd69"           "Fyn"            "Ehd3"           "Crip1"         
## [153] "Traf1"          "Ifngas1"        "Psmb10"         "Dennd2d"       
## [157] "Stk17b"         "Irf7"           "Slc17a9"        "Rps27rt"       
## [161] "Fam102a"        "Tgtp2"          "Il2rg"          "Card6"         
## [165] "Prkcq"          "Rgs3"           "Ncf4"           "Neurl3"        
## [169] "Flt3l"          "Arhgef3"        "Sh2d3c"         "Utrn"          
## [173] "Golm1"          "Prelid2"        "Pde7a"          "Otulinl"       
## [177] "Dock2"          "Bin1"           "Actr3"          "Tmem173"       
## [181] "9930111J21Rik2" "Ipcef1"         "Tent5c"         "H2-T23"        
## [185] "Dipk1a"         "Nod1"           "Crtam"          "Rabac1"        
## 
## $`2`
##   [1] "Ccna2"          "Nusap1"         "Birc5"          "Cdca3"         
##   [5] "Knl1"           "Mxd3"           "Tpx2"           "Cenpf"         
##   [9] "Plk1"           "Ckap2l"         "Kif11"          "Ube2c"         
##  [13] "Cdk1"           "Esco2"          "Aurkb"          "Prc1"          
##  [17] "Mki67"          "Cdca8"          "Cenpe"          "Ccnf"          
##  [21] "Tacc3"          "Spc25"          "Ccnb2"          "Sgo2a"         
##  [25] "Hmmr"           "Depdc1a"        "Shcbp1"         "Ttk"           
##  [29] "Kif15"          "Ccnb1"          "Bub1"           "Kif20a"        
##  [33] "Cks2"           "Neil3"          "Ncapg"          "Aurka"         
##  [37] "Kif22"          "Aspm"           "Depdc1b"        "Melk"          
##  [41] "Anln"           "Ndc80"          "Mis18bp1"       "Pimreg"        
##  [45] "Cdc20"          "Foxm1"          "Racgap1"        "Kif18b"        
##  [49] "Hist1h2ae"      "Kif4"           "Cep55"          "Bub1b"         
##  [53] "Nuf2"           "Lockd"          "Sgo1"           "Parpbp"        
##  [57] "Ska1"           "Cks1b"          "Cdca2"          "Ect2"          
##  [61] "Cdca5"          "Cenpm"          "Kif14"          "Nek2"          
##  [65] "Kif2c"          "Stil"           "Incenp"         "Cenpa"         
##  [69] "Ncaph"          "Hmgn2"          "Cenpp"          "Diaph3"        
##  [73] "Spag5"          "Pif1"           "Ncapd2"         "Cdkn3"         
##  [77] "Kpna2"          "Gm4316"         "Arhgef39"       "Prr11"         
##  [81] "H2afx"          "Ska3"           "Smc2"           "Kifc1"         
##  [85] "Cip2a"          "Kif23"          "Mad2l1"         "Ankle1"        
##  [89] "Knstrn"         "BC030867"       "Cit"            "Cdc25c"        
##  [93] "Plk4"           "Arhgap11a"      "Tmpo"           "Hist1h1b"      
##  [97] "Hist1h2ak"      "Dlgap5"         "Sapcd2"         "Rtkn2"         
## [101] "Ptma"           "Ckap2"          "Gtse1"          "Mastl"         
## [105] "Gm20628"        "Hist1h2ap"      "Kntc1"          "Kif18a"        
## [109] "Hmgb3"          "Ube2s"          "Espl1"          "Cenpi"         
## [113] "Anp32e"         "Kif20b"         "Hist1h2af"      "Hist1h3c"      
## [117] "Lmnb1"          "Iqgap3"         "Nucks1"         "Cdkn2c"        
## [121] "Hist2h2ac"      "Efcab11"        "Selenoh"        "Tubb4b"        
## [125] "Troap"          "Hist2h2bb"      "Fam83d"         "Hmgn5"         
## [129] "Zwilch"         "Mtfr2"          "Trip13"         "Poc1a"         
## [133] "Cenpl"          "Kifc5b"         "CAAA01147332.1" "Psrc1"         
## [137] "Hist1h3g"       "Ckap5"          "Hist1h4d"       "2610318N02Rik" 
## [141] "Eme1"           "Pttg1"          "H2afv"          "Hist1h1d"      
## [145] "Hist1h1e"       "Neurl1b"        "Arhgap19"       "Tubb5"         
## [149] "Trim59"         "Cdc25b"         "Spdl1"          "Ska2"          
## [153] "Dbf4"           "Hist1h2bm"      "Eldr"           "H1fx"          
## [157] "Gas2l3"         "Emp1"           "Bora"           "Nde1"          
## [161] "Hist1h3i"       "Hist2h4"        "Mns1"           "Tuba1c"        
## [165] "Rad21"          "Traip"          "Hist1h2bl"      "Hist1h3e"      
## [169] "Fzr1"           "Ddah2"          "Hist1h2bj"      "Bard1"         
## [173] "Dsn1"           "Gen1"           "Lsm5"          
## 
## $`3`
##   [1] "Top2a"    "Pclaf"    "Spc24"    "Rrm2"     "Fbxo5"    "Clspn"   
##   [7] "E2f8"     "Rad51ap1" "Tyms"     "Tk1"      "Hmgb2"    "Asf1b"   
##  [13] "Ncapg2"   "Lig1"     "E2f7"     "Uhrf1"    "Rrm1"     "Cdc45"   
##  [19] "Mcm5"     "Hist1h1a" "Tuba1b"   "Rad51"    "Tcf19"    "Mybl2"   
##  [25] "Oip5"     "Gmnn"     "Stmn1"    "Syce2"    "Cenpk"    "Cdc6"    
##  [31] "Ccne2"    "Fignl1"   "Pcna"     "Nt5dc2"   "Tipin"    "Cenpw"   
##  [37] "H2afz"    "Gm10282"  "Dut"      "Cenpn"    "Cenph"    "Mcm10"   
##  [43] "Dhfr"     "Fabp5"    "Mcm3"     "Mcm6"     "Siva1"    "Slbp"    
##  [49] "Rfc4"     "Chaf1a"   "Dnph1"    "Pole"     "Prim1"    "Dek"     
##  [55] "Pola1"    "Lrr1"     "Rcc1"     "Ticrr"    "Hells"    "Nsd2"    
##  [61] "Hirip3"   "Aunip"    "Brca1"    "Dctpp1"   "Atad2"    "Tfdp1"   
##  [67] "Dna2"     "Ccdc34"   "Ran"      "Brip1"    "Fen1"     "Nap1l1"  
##  [73] "Lsm2"     "Rad54l"   "Fancd2"   "Exo1"     "Ezh2"     "Gins2"   
##  [79] "Ranbp1"   "Alyref"   "Chtf18"   "Cenps"    "Slc43a3"  "Usp1"    
##  [85] "Anp32b"   "Acot7"    "Pold1"    "Psat1"    "Chek1"    "Snrpd1"  
##  [91] "Pkmyt1"   "Ube2t"    "Rfc5"     "Gins1"    "Phgdh"    "Fxn"     
##  [97] "Nrm"      "Dnmt1"    "Mcm7"     "Ung"      "Dscc1"    "Timeless"
## [103] "Zfp367"   "Rpa2"     "Snrpf"    "E2f1"     "Nasp"     "Ercc6l"  
## [109] "Shmt1"    "Pask"     "Banf1"    "Orc6"     "Rad54b"   "Hsp90aa1"
## [115] "Tmem107"  "Pa2g4"    "Tpi1"     "Mcm2"     "Dnajc9"   "Hmga1"   
## [121] "Ncapd3"   "Mcm4"     "Nelfe"    "Wdhd1"    "Ccne1"    "Rnaseh2b"
## [127] "Ppil1"    "Cntln"    "Chaf1b"   "Atad5"    "Rfc3"     "Pmf1"    
## [133] "Rps27l"   "Blm"      "Snu13"    "Lsm6"     "Slc29a1"  "Rpa3"    
## [139] "Atpif1"   "Rbbp7"    "Ptges3"   "Nutf2"    "Dbi"      "Ssrp1"   
## [145] "Hnrnpa3" 
## 
## $`4`
##   [1] "Rps24"         "Rps16"         "Rps20"         "Fau"          
##   [5] "Rps7"          "Rps10"         "Rps15a"        "Rps4x"        
##   [9] "Rpl13"         "Rps8"          "Rps5"          "Rps3a1"       
##  [13] "Rpsa"          "Rpl9"          "Rps27a"        "Rplp0"        
##  [17] "Rpl19"         "Rpl23"         "Rpl32"         "Rpl18a"       
##  [21] "Rpl30"         "Rpl18"         "Rps13"         "Rps3"         
##  [25] "Rps14"         "Rps26"         "Rpl39"         "Rpl37"        
##  [29] "Rpl21"         "Rpl34"         "Rpl41"         "Rpl8"         
##  [33] "Rplp1"         "Tpt1"          "Rpl17"         "Rplp2"        
##  [37] "Rpl27a"        "Rps11"         "Rpl6"          "Rps21"        
##  [41] "Rps19"         "Rpl12"         "Rpl35a"        "Rpl10"        
##  [45] "Rpl11"         "Rpl22"         "Rps2"          "Rps28"        
##  [49] "Rpl10a"        "Rps23"         "Rpl36a"        "Rps9"         
##  [53] "Rpl36"         "Rpl28"         "Gm10260"       "Rps27"        
##  [57] "Rpl15"         "Rpl3"          "Rpl37a"        "Rps12"        
##  [61] "Nme2"          "Rpl13a"        "Eef1b2"        "Rps29"        
##  [65] "Rpl38"         "Rpl35"         "Rpl24"         "Rack1"        
##  [69] "Rpl29"         "Rpl14"         "Rpl7"          "Rps6"         
##  [73] "Rpl22l1"       "Rpl26"         "Rpl27"         "Rpl5"         
##  [77] "Rpl7a"         "Naca"          "Eef2"          "Rps15"        
##  [81] "Npm1"          "Rac2"          "Rpl23a"        "Rpl4"         
##  [85] "Rpl36al"       "Rps25"         "Pabpc1"        "Eif3f"        
##  [89] "Atp5g2"        "Rpl31"         "Hspa8"         "Coro1a"       
##  [93] "Hsp90ab1"      "Btf3"          "Atp5e"         "Eef1d"        
##  [97] "Uba52"         "Rps18"         "Hint1"         "Eif3h"        
## [101] "Pfdn5"         "Fth1"          "Nsa2"          "Uqcrh"        
## [105] "Mif"           "Eif3k"         "Gstp1"         "Rps17"        
## [109] "Myl12b"        "Rexo2"         "Npc2"          "Fbl"          
## [113] "Psmb8"         "Cox8a"         "Snrpg"         "Eef1g"        
## [117] "Srm"           "Grcc10"        "Apex1"         "Hspe1"        
## [121] "Atp5l"         "Cox7a2l"       "Nop10"         "Ldha"         
## [125] "Tomm7"         "Eif1"          "Bola2"         "Sec61b"       
## [129] "Eif3i"         "2410006H16Rik" "Ppib"          "C1qbp"        
## [133] "Nme1"          "Ost4"          "Aprt"          "Krtcap2"      
## 
## $`5`
##  [1] "Ncr1"     "Tyrobp"   "Fcer1g"   "Klrk1"    "Klrb1c"   "Klre1"   
##  [7] "S1pr5"    "Plek"     "Klrb1a"   "Klri2"    "Gzma"     "Aoah"    
## [13] "Anxa1"    "Gzmb"     "Tbx21"    "Il18rap"  "Klra8"    "Klra3"   
## [19] "Klrb1f"   "Tnfsf12"  "Klrc1"    "Klrc2"    "Zeb2"     "Klra9"   
## [25] "Cma1"     "Itga2"    "Klra7"    "Arsb"     "Klra4"    "Fgl2"    
## [31] "Olfm1"    "Dapk2"    "Ccr2"     "Bhlhe40"  "Adamts14" "Klrb1b"  
## [37] "Cd244a"   "Fasl"     "Sytl3"    "Clnk"     "Scimp"    "Cd9"     
## [43] "Kcnj8"    "Ccl3"     "Id2"      "Gsap"     "Klrg1"    "Gem"     
## [49] "Ctla2b"   "Tmem37"   "Lrrk1"    "Arl4d"    "Il12rb2"  "Lat2"    
## [55] "Clip4"    "Styk1"    "Itgam"    "Plscr4"   "Cdk14"    "Klhl30"  
## [61] "Pik3ap1"  "Phactr3"  "Cdc20b"   "Sulf2"    "Ccl4"     "Osbpl3"  
## [67] "Fcgr2b"   "Cmklr1"   "Nrarp"    "Gas7"     "Rap1gap2" "Klri1"   
## [73] "Adgrl4"   "Tmem163"  "Gm33104"  "Rbpms"    "Sept5"    "Eya1"    
## [79] "Rac3"     "Pdgfb"    "Klrc3"    "Unc79"    "Itgax"    "Tnfaip2" 
## [85] "Gm19585"  "Rasl12"  
## 
## $`6`
##  [1] "Gtf2h4"        "Ldhb"          "Ctsl"          "Cd8a"         
##  [5] "Cd8b1"         "Dntt"          "Ccr9"          "Arpp21"       
##  [9] "Gm4258"        "Rag1"          "Cd4"           "Themis"       
## [13] "Glcci1"        "Satb1"         "Rmnd5a"        "Ccnd3"        
## [17] "Hmgb1"         "Spint2"        "Ets2"          "Endou"        
## [21] "Tcf7"          "Ap3s1"         "Trbc2"         "Trac"         
## [25] "Ssbp2"         "Arl5c"         "Ramp1"         "Chrna9"       
## [29] "Thy1"          "H3f3b"         "Rag2"          "Cyb5a"        
## [33] "Xrcc6"         "Rorc"          "Gm15340"       "Sox4"         
## [37] "Anxa2"         "Lck"           "Trbc1"         "Desi1"        
## [41] "H3f3a"         "Edem1"         "Ly6d"          "Znrf1"        
## [45] "Malat1"        "Myb"           "Colq"          "Camk4"        
## [49] "Sla"           "Mier1"         "Lat"           "Sh2d1a"       
## [53] "Gm38405"       "Xrra1"         "Slc16a5"       "Tcf12"        
## [57] "Trp53inp1"     "Atl2"          "Btg2"          "Rsrp1"        
## [61] "2610307P16Rik" "Ntrk3"         "Abi3"          "Ly6e"         
## [65] "Rgcc"          "Prrt1"         "Mad1l1"        "Dck"          
## [69] "Prkcb"         "Tctex1d1"      "Nebl"          "Cd3e"         
## [73] "Clk3"          "Agfg2"         "Stx6"          "F13a1"        
## [77] "Trp53i11"      "Cdca7"         "Zfp280d"       "Cux1"         
## [81] "P2rx1"        
## 
## $`7`
##  [1] "Nkg7"          "Ctsw"          "Il2rb"         "Prf1"         
##  [5] "Ifitm10"       "Eomes"         "Samd3"         "Cd7"          
##  [9] "Cst7"          "Ctla2a"        "Ccr5"          "Zyx"          
## [13] "Cxcr6"         "Hopx"          "1700025G04Rik" "Xcl1"         
## [17] "Lsamp"        
## 
## $`8`
##  [1] "1500009L16Rik" "Ifitm2"        "Myl10"         "Gm4632"       
##  [5] "Il2ra"         "Uaca"          "Ccdc18"        "2700054A10Rik"
##  [9] "Ptcra"         "Fkbp5"         "Fads2"         "Epb41l4b"     
## [13] "Myc"          
## 
## $`9`
##  [1] "Zbtb16"  "Tcrg-V1" "Trpm6"   "Fam129a" "Il4"     "Vdr"     "Izumo1r"
##  [8] "Ccr10"   "Ccn4"    "Chn2"    "Gfra4"  
## 
## $`10`
## [1] "Ccl5"    "Klrd1"   "Myo1f"   "Pglyrp1" "Slamf7"  "Ly6c2"   "Ly6c1"  
## 
## $`11`
## [1] "Actb"     "Pfn1"     "Actg1"    "Arhgdib"  "Cfl1"     "Sh3bgrl3" "Serf2"   
## 
## $`12`
## [1] "Tcrg-V4" "Trgv2"   "Tcrg-C4" "Tcrg-C2" "Tcrg-C1" "Pdcd1"   "Plac8"  
## 
## $`13`
## [1] "Il23r"     "Pxdc1"     "Mmp25"     "Serpinb1a" "Ccr6"      "Gm15868"  
## [7] "Adamts2"
Idents(miceWT)<-"manual.annotation"
miceWT@active.ident <- factor(miceWT@active.ident,levels=c("DN","DPblast","DPsm-CD25+","DPsm-CCR7+","DPsm","DP69int","DP69+","SP4","SP8","Tgd","NK"))
plot_ggheatmap(miceWT_scigenex20.3, 
               use_top_genes = FALSE,
               ident=Idents(miceWT)) + ggtitle("Heatmap of Co-Expressed Gene Modules Identified by SciGeneX (k = 20, inflation= 3)")

miceWT_scigenex20.3 <- enrich_go(miceWT_scigenex20.3, specie = "Mmusculus", ontology = "BP")
plot_clust_enrichments(miceWT_scigenex20.3, gradient_palette=colors_for_gradient("Je1"), 
                       floor=50,
                       nb_go_term = 2) + 
    theme(axis.text.y = element_text(size=12))

#Assign cell types to cells in merged object based on scigeneX’s gene modules and ADT data

palette1 <- as.character(paletteer::paletteer_d("ggsci::green_material", n = 10))
names(palette1) <- c("DN","DPblast(WT)","DPsm(WT)","DPsmCD25+(WT)","DPsmCCR7+(WT)","DP69(WT)","SP8(WT)","SP8CD69+(WT)","SP4(WT)","SP4CD69+(WT)")
palette2 <- as.character(rev(paletteer::paletteer_d("ggsci::red_material", n = 4)))
names(palette2) <- c("DPblast Myc+","DPsm Myc+","DP69 Myc+","SP8 Myc+")
palette3 <- c("#7CB342FF","#689F38FF","#558B2FFF","#33691EFF")
names(palette3) <- c("NK","Tgd early","Tgd mature","MAIT")
palette4 <- as.character(paletteer::paletteer_d("ggsci::uniform_startrek", n = 1))
names(palette4) <- "Myc+"
ggplotly(DimPlot(bc.combined.cc, group.by = "sig.annotation", reduction = "wnn.umap", cols = c(palette1,palette2,palette3,palette4), label =T, label.color = "black",label.size = 5, pt.size = 0.5, repel =TRUE))
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

BALB/c TCR analysis

#Script : Immcantation_BalBC.Rmd
OTIIpalette <- c("#FDE725FF","#414487FF","#DE4968FF","#22A884FF","#7AD151FF","#808080FF")
names(OTIIpalette) <- c("OTII","OTII - TCRB incomplete","OTII - TCRA incomplete","OTII multichains","non OTII","unknown")
DimPlot(bc.combined.cc, group.by = "OTIIstatus",split.by = "OTIIstatus", reduction = "wnn.umap", cols = OTIIpalette, pt.size = 0.5)